27 Sep

New publication from the lab: Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26

The TRIM-NHL protein Meiotic-P26 acts as a regulator of cell fate in Drosophila. Its activity is critical for ovarian germline stem cell maintenance, differentiation of oocytes and spermatogenesis. Together with our collaborators from the Glatt lab (Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University Krakow, Poland) and the Bujnicki lab (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Poland), we could solve the first high resolution structure of the Mei-P26 NHL domain and define a consensus RNA motif that it recognizes. Molecular dynamics simulations allowed us to predict and subsequently experimentally validate key amino acid residues involved specific RNA recognition, highlighting differences to other NHL domains. Using individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP), we could identify RNA targets of Mei-P26 in cultured Drosophila cells and demonstrate the protein can either repress or activate its genuine mRNA targets. Regulation requires the NHL domain of the protein but is independent of its function as a ubiquitin ligase.

In particular, the last finding significantly expands our understanding of TRIM-NHL protein-mediated gene regulation. These proteins were previously considered to exclusively act as repressors of gene expression. Strikingly, Mei-P26 itself appears to lack any regulatory activity suggesting that the regulatory outcome is determined by the recruitment of different co-factors, some of which have previously been identified by genetic means.

A preprint of the manuscript is available at bioRxiv (doi.org/10.1101/2021.09.20.461029)

22 Jul

Congratulations: Andreas defended his PhD

On Tuesday, July 20th Andreas Horn very successfully defended his PhD thesis. For many years, Andreas was advancing our understanding of how RNA binding proteins control development and cell fate decisions in the model organism Drosophila melanogaster. We are very proud and happy about Andreas’ success and we wish him all the best for his future endeavors.

30 May

EMBO practical course: Measuring translational dynamics by ribosome profiling

After being postponed due to the Coronavirus pandemic, the EMBO practical course on measuring translational dynamics by ribosome profiling could finally take place from May 17th to 25th 2021 in a virtual format. 16 participants from research labs across the globe discussed intensively with ten speakers and 12 trainers about how to perform ribosome profiling experiments. Pre-recorded talks provided insight into the different aspects of the technique and used recent examples to illustrate how ribosome profiling can be used to further our understanding of translation and its regulation. Furthermore, Pavel ‘Pasha’ Baranov and his team from the University College Cork provided an excellent online tutorial on the bioinformatic analyses of ribosome data.

I am particular grateful  for the insightful talks provided by Nicholas Ingolia (UC Berkeley), Marina Rodnina (MPI Göttingen), Rachel Green (Johns Hopkins), Anne Willis (University of Cambridge), Thomas Preiss (Australia National University), Gerben Menschaert (Ghent University), and Vladimir Benes (EMBL Heidelberg) that made the curse a big success. Also, on behalf of all organizers, I would like to thank Lisa Trinh, Diah Yulianti, Irena Provaznikova (from the EMBL Courses and Conferences Office) and in particular Yvonne Yeboah (form the EMBL teaching lab) for their daily support. Finally, without the expertise of my co-organizers Elisabeth Zielonka (EMBL Heidelberg), Sebastian Leidel (University of Bern), and Pavel ‘Pasha’ Baranov (University College Cork) it would not have been possible to host this course.

Above: Short explanatory movie on ribosome profiling. I would like to thank Daniel Krüger, Julia Schleisiek, Claudiu Grozea, and in particular Yvonne Yeboah and Sebastian Leidel for production of the video. More information on the movie can be found here.

25 Feb

Open Position

Are you excited about biomedical research? Do you want to employ state-of-the-art methodology with the aim to unerstand how tumor cells become resistant to treatment? Do you want to work in a stimulating research environment with great colleagues? Then this is the right job for you:

We are looking for a Technical Assistant to perform ribosome profiling experiments in the context of cellular stress and resistance to chemotherapeutic treatment. Click here for more information (PDF, german).

Please feel free to contact us any time for more details…

18 Oct

New publication from the lab: multi-omics to unravel stress-dependent gene expression changes

Together with our collaborator Robert Ahrends (at the Universität Wien), we published a summary of our recent work in the BIOspektrum journal. We describe how multi-omics approaches can yield novel and clinically relevant insights into stress-mediated gene expression changes. The article (in German) can be accessed here. The work has been a close collaboration within the BMBF-funded junior research consortium Systems Biology of the Unfolded Proteins Response in Glioma (SUPR-G).

10 Oct

Congratulations: Stefan defended his PhD

On Friday, October 9th Stefan Reich very successfully defended his PhD thesis. For many years, Stefan was the driving force of the project Systems Biology of the Unfolded Protein Response in Glioma (SUPR-G) and discovered that the UPR can elicit resistance to treatment with folate-based antimetabolites (click here for the publication). We are very proud and happy about Stefan’s success and we wish him all the best for his future endeavors.

9 Jul

New publication from the lab: Cell stress induces chemoresistance

A combination of high-throughput analyses uncovers novel mechanism of stress-induced chemoresistance

Resistance of cancer cells against therapeutic agents is a major cause of treatment failure, especially in recurrent diseases. In a collaborative effort with the labs of Robert Ahrends, Björn Tews, Grischa Tödt and Christiane Knobbe-Thomsen, we identified a novel mechanism of chemoresistance which has now been published in ‘Nature Communications’. It is driven by the Unfolded Protein Response (UPR), a cellular stress response pathway that alters gene expression and cellular metabolism to promote cell survival under stress.


The Unfolded Protein Response (UPR), an important cellular stress response pathway, does not only contribute to cancer development, progression and chemoresistance, but also it plays an important role in numerous other diseases, among them diabetes and neurodegenerative disorders such as Alzheimer’s disease. A detailed biochemical understanding of the UPR is critically required to better define its role in disease and to develop novel therapeutic strategies. To produce a comprehensive description of the UPR, we employed a ‘multi-omics’ approach, combining large datasets from genetics and proteomics. This allowed us to define a list of genes (the UPR regulon) that are activated to promote cell survival under stress. Besides the previously known factors, we identified numerous genes that have not previously been implicated in stress response pathways and many of them have key functions in cancer development and cellular metabolism.

Schematic overview over the Unfolded Protein Response (UPR)

Changes in cellular metabolism are a hallmark of cancer cells and allow to sustain rapid tumor growth. Chemotherapy often aims at interfering with these metabolic pathways. We demonstrated that stress-mediated genetic regulation of enzymes involved in amino acid biosynthesis and one-carbon (1C) metabolism that relies on the vitamin folate as a cofactor. Moreover, upon stress, cancer cells become fully resistant to chemotherapeutic agents which target this specific metabolic pathway. This includes Methotrexate, a drug commonly employed in the treatment of cancer and rheumatic disease. Detailed biochemical and genetic investigations revealed that resistance is driven by a previously unrecognized mechanism. Its precise molecular characterization might lead to novel therapeutic concepts aimed at overcoming chemoresistance n cancer therapy.

Publication:

Reich S, Nguyen CDL, Has C, Steltgens S, Soni H, Coman C, Freyberg M, Bichler A, Seifert N, Conrad D, Knobbe-Thomsen CB, Tews B, Toedt G, Ahrends R, and Medenbach J: A multi-omics analysis reveals the unfolded protein response regulon and stress-induced resistance to folate-based antimetabolites – in Nature Communications, DOI:10.1038/s41467-020-16747-y

Press releases:

 

19 Mar

CANCELED: EMBO Practical Course on Measuring Translational Dynamics by Ribosome Profiling

It is with heavy heart that we have to inform you that EMBL Heidelberg and the scientific organisers have decided to postpone the EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling 2020.

We have taken this difficult decision in order to better play our part in reducing the impact and spread of the novel coronavirus and also in recognition of the fact that many of our speakers and participants are currently finding it difficult to travel.

The new date for this course is still under discussion and will be communicated once it has been agreed.

5 Mar

June 2nd, 2020 – Guest Speaker: Sebastian Maurer

UPDATE – the seminar has been postponed to June 2nd 2020 (mark your calendar – you don’t want to miss out on the exciting data and findings that Sebastian is going to present!)

TALK CANCELED – Unfortunately Sebastian cannot make it on October 17th. We are trying to postpone the talk – stay tuned for updates…

Wenn du Tore schießen möchtest, musst du an der richtigen Stelle stehen’ (if you want to score goals you have to be in the right spot) – that’s what children get taught by their football trainers. If you want to be ‘the fox in the box’ positioning is very important.

This is also true for RNAs. Many mRNAs exhibit a specific sub-cellular localization allowing localized production of proteins. This is of importance in many biological settings: e.g. it equips synapses with a unique proteome, allows directed cell migration, and determines the body axes during early embryonic development.

In mammalian neurons, the asymmetric distribution of mRNAs and local protein synthesis is required for essential processes as cell polarization, migration and synaptic plasticity underlying long-term memory formation. However, the essential components driving cytoplasmic mRNA transport in neurons and mammalian cells are not known.

Mark your calendars: On October 17th at 2p.m. in H53, Sebastian Maurer from the Centre for Genomic regulation (CRG) in Barcelona, Spain, will report the first reconstitution of a mammalian mRNA transport system. His studies reveal that the tumour suppressor adenomatous polyposis coli (APC) forms stable complexes with the axonally localised b-actin and b2B-tubulin mRNAs which are linked to a heterotrimeric kinesin-2 via the cargo adaptor KAP3. APC activates kinesin-2 and both proteins are sufficient to drive specific transport of defined mRNA packages. Guanine-rich sequences located in 3’UTRs of axonal mRNAs increase transport efficiency and balance the access of different mRNAs to the transport system. These findings establish for the first time a minimal set of proteins capable of driving kinesin-based, mammalian mRNA transport.

2 Mar

New publication: U2AF26 and U2AF35 as regulators of translation

A function in splicing versus a function in translational control – why not both?

U2AF proteins are best known for their functions in spliceosomal processing of pre-mRNAs where a homodimer of U2AF65 and U2AF35 functions in recognition of the 3′ splice site. The smaller subunit, U2AF35, contains two zinc fingers (ZnFs). Mutations therein have recently been associated with malignant transformation. The molecular function(s) of the two domains have, however, not been studied in great detail.

A collaborative effort, spearheaded by the Heyd lab at the Free University of Berlin, now revealed that the two ZnFs have remarkably different activity. Both are required for splicing regulation, whereas only ZnF2 controls protein stability and contributes to the interaction with U2AF65.

Intriguingly, a naturally occuring splice variant of U2AF26, a paralog of U2AF35, lacks the second ZnF. It is upregulated upon activation of primary mouse T cells and localizes to the cytoplasm, suggesting a splicing-independent function. Employing ribosome profiling in a model T cell line, we provide evidence for a role of U2AF26 in activating cytoplasmic steps in gene expression, notably translation. Consistently, an MS2 tethering assay shows that cytoplasmic U2AF26/35 increases translation when localized to the 5ʹUTR of a model mRNA. This regulation is partially dependent on ZnF1 thus providing a connection between a core splicing factor, the ZnF domains and the regulation of translation. Altogether, our work reveals unexpected functions of U2AF26/35 in mammalian cells beyond the regulation of splicing.

Check out the exciting paper in RNA Biology: https://doi.org/10.1080/15476286.2020.1732701

21 Feb

February 25th, 2020 – Guest Speaker: Sebastian Leidel

tRNA modifications – Connecting translation dynamics to cellular quality control

On february 25th, 2020, at 5 p.m., Sebastian Leidel from the University of Bern will give a talk in H53. Sebastian and his lab have pioneered the use of ribosome profiling to understand the importance of tRNA modifications in translation.

tRNAs are key players in mRNA translation linking amino acids to a specific codon sequence. Interestingly, tRNA molecules carry a plethora of chemical modifications of their nucleotides, which are posttranscriptionally introduced by many different enzymatic pathways. Even though huge progress has been made, it is still unclear how most of these tRNA modifications contribute to cellular function. This is of particular importance as GWAS studies have linked different modification pathways to a number of degenerative diseases and cancer. New technologies explored by Sebastian and his lab have provided novel insights into this exciting research field.

We are looking forward to seeing you on Tuesday for an evening of exciting science!

16 Dec

New lab member: Andreas Meindl

Andreas Meindl has just joined the lab as a PhD student. Andreas will work on the function of Sex-lethal in Drosophila melanogaster sexual development addressing in detail its auto-regulatory feedback to splicing. Welcome to the lab!

2 Dec

Open position: Technical Assistant

You want to work on exciting and diverse research projects employing state-of-the-art methodologies? You want to join a young and highly motivated team? Then get your CVs ready, there is a job opening for a Technical Assistant!

The basic information: Salary TV-L E9, starting date as soon as possible, application deadline December 22nd 2019.

For more information (in German) please click here.

1 Dec

January 30th, 2020 – Guest Speaker: Florian Heyd

Some like it cold: (Body)temperature-controlled kinase activity in circadian biology, sex determination and beyond

In numerous animals (including crocodiles, alligators, tortoises, and some teleost fish), sex is determined independently of the genotype. Rather the temperature experienced during embryonic or larval stages results in the development of phenotypically male or female animals. Exemplarily, exposing alligator eggs to elevated temperatures produces mostly male offspring. The mechanism by which subtle changes in temperature are sensed to govern sex-specific development, however, has remained elusive.

On January 30th 2020 (2p.m. in H53), Florian Heyd from the Freie Universität Berlin will talk about protein kinases that act as very sensitive thermo-sensors to control changes to alternative splicing. The exciting work combines enzymology, structural-, and RNA biology to reveal in molecular detail how the activity of CDC-like kinases (CLKs) is altered by changes in temperature, resulting in differential phosphorylation of SR-proteins and subsequently in altered splicing patterns.

 

Click here for the advertisement of the talk.

 

5 Nov

SFB960 PIs in 2019

The Collaborative Research Centre 960 (SFB960) ‘RNP biogenesis: assembly of ribosomes and non-ribosomal RNPs and control of their function’ has recently been awarded funding for another four years (see this post). The 18 group leaders (pictuerd below) will head 16 research and 3 service projects and a graduate school.

We are looking forward to four more years of collaborative research and exciting new findings.

Principal Investigators third funding period (from left to right): J. Medenbach, J. Griesenbeck, T. Heise, P. Milkereit, W. Seufert, A. Bruckmann, S. Ferreira-Cerca, M. Kretz, J. Perez-Fernandez, T. Dresselhaus, G. Längst, R. Sprangers, H. Tschochner, D. Grohmann, and C. Engel;
missing on the photo: G. Sommer, S. Sprunck, G. Meister, K. Grasser